Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000540732
Querying Taster for transcript #2: ENST00000269980
Querying Taster for transcript #3: ENST00000457836
MT speed 0 s - this script 2.163737 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BCKDHAdisease_causing_automatic0.999999998241364simple_aae0Y438Nsingle base exchangers137852870show file
BCKDHAdisease_causing_automatic0.999999999711439simple_aae0Y441Nsingle base exchangers137852870show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999998241364 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM124305)
  • known disease mutation at this position (HGMD CM890022)
  • known disease mutation: rs100009 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:41930487T>AN/A show variant in all transcripts   IGV
HGNC symbol BCKDHA
Ensembl transcript ID ENST00000269980
Genbank transcript ID NM_000709
UniProt peptide P12694
alteration type single base exchange
alteration region CDS
DNA changes c.1312T>A
cDNA.1680T>A
g.27123T>A
AA changes Y438N Score: 142 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 438
frameshift no
known variant Reference ID: rs137852870
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs100009 (pathogenic for Maple syrup urine disease|Maple syrup urine disease type 1A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890022)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7331
4.7821
(flanking)4.7821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 145
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      438LARHLQTYGEHYPLDHFDK*
mutated  not conserved    438LARHLQTYGEHNPLDHFDK
Ptroglodytes  all identical  ENSPTRG00000011025  438LARHLQTYGEHYPLDHFDK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000060376  439LARHLQTYGEHYPLDHFDK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009706  439MWRHVQQYKEHYPVDLYEK
Drerio  all identical  ENSDARG00000040555  439QQYKEHYPLDHYEK
Dmelanogaster  all identical  FBgn0037709  432LEKHIEAHKEHYPLKDFEK
Celegans  all identical  Y39E4A.3  422LDAHVAEYKEHYPM
Xtropicalis  all identical  ENSXETG00000018753  401LMKHLKLYGEHYPLDSYEK
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1338 / 1338
position (AA) of stopcodon in wt / mu AA sequence 446 / 446
position of stopcodon in wt / mu cDNA 1706 / 1706
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 369 / 369
chromosome 19
strand 1
last intron/exon boundary 1536
theoretical NMD boundary in CDS 1117
length of CDS 1338
coding sequence (CDS) position 1312
cDNA position
(for ins/del: last normal base / first normal base)		 1680
gDNA position
(for ins/del: last normal base / first normal base)		 27123
chromosomal position
(for ins/del: last normal base / first normal base)		 41930487
original gDNA sequence snippet TGCAGACCTACGGGGAGCACTACCCACTGGATCACTTCGAT
altered gDNA sequence snippet TGCAGACCTACGGGGAGCACAACCCACTGGATCACTTCGAT
original cDNA sequence snippet TGCAGACCTACGGGGAGCACTACCCACTGGATCACTTCGAT
altered cDNA sequence snippet TGCAGACCTACGGGGAGCACAACCCACTGGATCACTTCGAT
wildtype AA sequence MAVAIAAARV WRLNRGLSQA ALLLLRQPGA RGLARSHPPR QQQQFSSLDD KPQFPGASAE
FIDKLEFIQP NVISGIPIYR VMDRQGQIIN PSEDPHLPKE KVLKLYKSMT LLNTMDRILY
ESQRQGRISF YMTNYGEEGT HVGSAAALDN TDLVFGQYRE AGVLMYRDYP LELFMAQCYG
NISDLGKGRQ MPVHYGCKER HFVTISSPLA TQIPQAVGAA YAAKRANANR VVICYFGEGA
ASEGDAHAGF NFAATLECPI IFFCRNNGYA ISTPTSEQYR GDGIAARGPG YGIMSIRVDG
NDVFAVYNAT KEARRRAVAE NQPFLIEAMT YRIGHHSTSD DSSAYRSVDE VNYWDKQDHP
ISRLRHYLLS QGWWDEEQEK AWRKQSRRKV MEAFEQAERK PKPNPNLLFS DVYQEMPAQL
RKQQESLARH LQTYGEHYPL DHFDK*
mutated AA sequence MAVAIAAARV WRLNRGLSQA ALLLLRQPGA RGLARSHPPR QQQQFSSLDD KPQFPGASAE
FIDKLEFIQP NVISGIPIYR VMDRQGQIIN PSEDPHLPKE KVLKLYKSMT LLNTMDRILY
ESQRQGRISF YMTNYGEEGT HVGSAAALDN TDLVFGQYRE AGVLMYRDYP LELFMAQCYG
NISDLGKGRQ MPVHYGCKER HFVTISSPLA TQIPQAVGAA YAAKRANANR VVICYFGEGA
ASEGDAHAGF NFAATLECPI IFFCRNNGYA ISTPTSEQYR GDGIAARGPG YGIMSIRVDG
NDVFAVYNAT KEARRRAVAE NQPFLIEAMT YRIGHHSTSD DSSAYRSVDE VNYWDKQDHP
ISRLRHYLLS QGWWDEEQEK AWRKQSRRKV MEAFEQAERK PKPNPNLLFS DVYQEMPAQL
RKQQESLARH LQTYGEHNPL DHFDK*
speed 0.10 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999711439 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM124305)
  • known disease mutation at this position (HGMD CM890022)
  • known disease mutation: rs100009 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:41930487T>AN/A show variant in all transcripts   IGV
HGNC symbol BCKDHA
Ensembl transcript ID ENST00000457836
Genbank transcript ID N/A
UniProt peptide P12694
alteration type single base exchange
alteration region CDS
DNA changes c.1321T>A
cDNA.1326T>A
g.27123T>A
AA changes Y441N Score: 142 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 441
frameshift no
known variant Reference ID: rs137852870
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs100009 (pathogenic for Maple syrup urine disease|Maple syrup urine disease type 1A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890022)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890022)
known disease mutation at this position, please check HGMD for details (HGMD ID CM124305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890022)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7331
4.7821
(flanking)4.7821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 145
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      441LARHLQTYGEHYPLDHFDK*
mutated  not conserved    441LARHLQTYGEHNPLDHFDK
Ptroglodytes  all identical  ENSPTRG00000011025  438LARHLQTYGEHYPLDHFDK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000060376  439LARHLQTYGEHYPLDHFDK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009706  439HYPVDLYEK
Drerio  all identical  ENSDARG00000040555  439MWRHVQQYKEHYPLDHYEK
Dmelanogaster  all identical  FBgn0037709  432LEKHIEAHKEHYPLK
Celegans  all identical  Y39E4A.3  422LDAHVAEYKEHYPM
Xtropicalis  all identical  ENSXETG00000018753  401YGEHYPLDSYEK
protein features
start (aa)end (aa)featuredetails 
440442HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1347 / 1347
position (AA) of stopcodon in wt / mu AA sequence 449 / 449
position of stopcodon in wt / mu cDNA 1352 / 1352
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 6 / 6
chromosome 19
strand 1
last intron/exon boundary 1182
theoretical NMD boundary in CDS 1126
length of CDS 1347
coding sequence (CDS) position 1321
cDNA position
(for ins/del: last normal base / first normal base)		 1326
gDNA position
(for ins/del: last normal base / first normal base)		 27123
chromosomal position
(for ins/del: last normal base / first normal base)		 41930487
original gDNA sequence snippet TGCAGACCTACGGGGAGCACTACCCACTGGATCACTTCGAT
altered gDNA sequence snippet TGCAGACCTACGGGGAGCACAACCCACTGGATCACTTCGAT
original cDNA sequence snippet TGCAGACCTACGGGGAGCACTACCCACTGGATCACTTCGAT
altered cDNA sequence snippet TGCAGACCTACGGGGAGCACAACCCACTGGATCACTTCGAT
wildtype AA sequence MAVAIAAARV WRLNRGLSQQ QQFSSLDDKP QFPGASAEFI DKLEFIQPNV ISGIPIYRVM
DRQGQIINPS EDPHLPKEKV LKLYKSMTLL NTMDRILYES QRQGRISFYM TNYGEEGTHV
GSAAALDNTD LVFGQYREAG VLMYRDYPLE LFMAQCYGNI SDLGKGRQMP VHYGCKERHF
VTISSPLATQ IPQAVGAAYA AKRANANRVV ICYFGEGAAS EGDAHAGFNF AATLECPIIF
FCRNNGYAIS TPTSEQYRGD GIAARGPGYG IMSIRVDGND VFAVYNATKE ARRRAVAENQ
PFLIEAMTYS SSPILPPDPH SREPTLTWGP LPLCRIGHHS TSDDSSAYRS VDEVNYWDKQ
DHPISRLRHY LLSQGWWDEE QEKAWRKQSR RKVMEAFEQA ERKPKPNPNL LFSDVYQEMP
AQLRKQQESL ARHLQTYGEH YPLDHFDK*
mutated AA sequence MAVAIAAARV WRLNRGLSQQ QQFSSLDDKP QFPGASAEFI DKLEFIQPNV ISGIPIYRVM
DRQGQIINPS EDPHLPKEKV LKLYKSMTLL NTMDRILYES QRQGRISFYM TNYGEEGTHV
GSAAALDNTD LVFGQYREAG VLMYRDYPLE LFMAQCYGNI SDLGKGRQMP VHYGCKERHF
VTISSPLATQ IPQAVGAAYA AKRANANRVV ICYFGEGAAS EGDAHAGFNF AATLECPIIF
FCRNNGYAIS TPTSEQYRGD GIAARGPGYG IMSIRVDGND VFAVYNATKE ARRRAVAENQ
PFLIEAMTYS SSPILPPDPH SREPTLTWGP LPLCRIGHHS TSDDSSAYRS VDEVNYWDKQ
DHPISRLRHY LLSQGWWDEE QEKAWRKQSR RKVMEAFEQA ERKPKPNPNL LFSDVYQEMP
AQLRKQQESL ARHLQTYGEH NPLDHFDK*
speed 0.10 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

Problems

data problem

back to results table